Ultra-fast scalable estimation of single-cell differentiation potency from scRNA-Seq data.

MOTIVATION: An important task in the analysis of single-cell RNA-Seq data is the estimation of differentiation potency, as this can help identify stem-or-multipotent cells in non-temporal studies or in tissues where differentiation hierarchies are not well established. A key challenge in the estimation of single-cell potency is the need for a fast and accurate algorithm, scalable to large scRNA-Seq studies profiling millions of cells. RESULTS: Here, we present a single-cell potency measure, called Correlation of Connectome and Transcriptome (CCAT), which can return accurate single-cell potency estimates of a million cells in minutes, a 100-fold improvement over current state-of-the-art methods. We benchmark CCAT against 8 other single-cell potency models and across 28 scRNA-Seq studies, encompassing over 2 million cells, demonstrating comparable accuracy than the current state-of-the-art, at a significantly reduced computational cost, and with increased robustness to dropouts. AVAILABILITY AND IMPLEMENTATION: CCAT is part of the SCENT R-package, freely available from https://github.com/aet21/SCENT. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Hierarchical Post-transcriptional Regulation of Colicin E2 Expression in Escherichia coli.

Post-transcriptional regulation of gene expression plays a crucial role in many bacterial pathways. In particular, the translation of mRNA can be regulated by trans-acting, small, non-coding RNAs (sRNAs) or mRNA-binding proteins, each of which has been successfully treated theoretically using two-component models. An important system that includes a combination of these modes of post-transcriptional regulation is the Colicin E2 system. DNA damage, by triggering the SOS response, leads to the heterogeneous expression of the Colicin E2 operon including the cea gene encoding the toxin colicin E2, and the cel gene that codes for the induction of cell lysis and release of colicin. Although previous studies have uncovered the system's basic regulatory interactions, its dynamical behavior is still unknown. Here, we develop a simple, yet comprehensive, mathematical model of the colicin E2 regulatory network, and study its dynamics. Its post-transcriptional regulation can be reduced to three hierarchically ordered components: the mRNA including the cel gene, the mRNA-binding protein CsrA, and an effective sRNA that regulates CsrA. We demonstrate that the stationary state of this system exhibits a pronounced threshold in the abundance of free mRNA. As post-transcriptional regulation is known to be noisy, we performed a detailed stochastic analysis, and found fluctuations to be largest at production rates close to the threshold. The magnitude of fluctuations can be tuned by the rate of production of the sRNA. To study the dynamics in response to an SOS signal, we incorporated the LexA-RecA SOS response network into our model. We found that CsrA regulation filtered out short-lived activation peaks and caused a delay in lysis gene expression for prolonged SOS signals, which is also seen in experiments. Moreover, we showed that a stochastic SOS signal creates a broad lysis time distribution. Our model thus theoretically describes Colicin E2 expression dynamics in detail and reveals the importance of the specific regulatory components for the timing of toxin release.

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.

MOTIVATION: The Illumina Infinium 450 k DNA Methylation Beadchip is a prime candidate technology for Epigenome-Wide Association Studies (EWAS). However, a difficulty associated with these beadarrays is that probes come in two different designs, characterized by widely different DNA methylation distributions and dynamic range, which may bias downstream analyses. A key statistical issue is therefore how best to adjust for the two different probe designs. RESULTS: Here we propose a novel model-based intra-array normalization strategy for 450 k data, called BMIQ (Beta MIxture Quantile dilation), to adjust the beta-values of type2 design probes into a statistical distribution characteristic of type1 probes. The strategy involves application of a three-state beta-mixture model to assign probes to methylation states, subsequent transformation of probabilities into quantiles and finally a methylation-dependent dilation transformation to preserve the monotonicity and continuity of the data. We validate our method on cell-line data, fresh frozen and paraffin-embedded tumour tissue samples and demonstrate that BMIQ compares favourably with two competing methods. Specifically, we show that BMIQ improves the robustness of the normalization procedure, reduces the technical variation and bias of type2 probe values and successfully eliminates the type1 enrichment bias caused by the lower dynamic range of type2 probes. BMIQ will be useful as a preprocessing step for any study using the Illumina Infinium 450 k platform. AVAILABILITY: BMIQ is freely available from http://code.google.com/p/bmiq/. CONTACT: a.teschendorff@ucl.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Neuromodulation in Pediatric Migraine using Repetitive Neuromuscular Magnetic Stimulation: A Feasibility Study.

Migraine has a relevant impact on pediatric health. Non-pharmacological modalities for its management are urgently needed. This study assessed the safety, feasibility, acceptance, and efficacy of repetitive neuromuscular magnetic stimulation (rNMS) in pediatric migraine. A total of 13 patients with migraine, ≥6 headache days during baseline, and ≥1 myofascial trigger point in the upper trapezius muscles (UTM) received six rNMS sessions within 3 weeks. Headache frequency, intensity, and medication intake were monitored using headache calendars; headache-related impairment and quality of life were measured using PedMIDAS and KINDL questionnaires. Muscular involvement was assessed using pressure pain thresholds (PPT). Adherence yielded 100%. In 82% of all rNMS sessions, no side effects occurred. All participants would recommend rNMS and would repeat it. Headache frequency, medication intake, and PedMIDAS scores decreased from baseline to follow-up (FU), trending towards statistical significance (p = 0.089; p = 0.081, p = 0.055). A total of 7 patients were classified as responders, with a ≥25% relative reduction in headache frequency. PPT above the UTM significantly increased from pre- to post-assessment, which sustained until FU (p = 0.015 and 0.026, respectively). rNMS was safe, feasible, well-accepted, and beneficial on the muscular level. The potential to reduce headache-related symptoms together with PPT changes of the targeted UTM may underscore the interplay of peripheral and central mechanisms conceptualized within the trigemino-cervical complex.

Repetitive neuromuscular magnetic stimulation in children with headache.

INTRODUCTION: Repetitive neuromuscular magnetic stimulation (rNMS) was previously applied in adult patients with episodic migraine, showing beneficial effects on headache characteristics, high safety, and convincing satisfaction. This study aims to assess rNMS as a personalized intervention in pediatric headache. METHODS: Retrospective chart review including patients with migraine, TTH, mixed type headache, or PTH, who had received at least one test rNMS session targeting the upper trapezius muscles (UTM). RESULTS: 33 patients (13.9 ± 2.5 years; 61% females) were included in the primary analysis, resulting in a total of 182 rNMS sessions. 43 adverse events were documented for 40 of those sessions (22%). Most common side effects were tingling (32.6%), muscle sore (25.5%), shoulder (9.3%) and back pain (9.3%). Secondly, in patients (n = 20) undergoing the intervention, headache frequency (p = 0.017) and minimum and maximum intensities (p = 0.017; p = 0.023) significantly decreased from baseline to 3-month after intervention. 11 patients (44%) were classified as ≥25% responders, with 7 patients (28%) experiencing a ≥75% reduction of headache days. After 73% of interventions, patients reported rNMS helped very well or well. A majority of patients would repeat (88.5%) and recommend rNMS (96.2%) to other patients. CONCLUSION: rNMS seems to meet the criteria of safety, feasibility, and acceptance among children and adolescents with three age-typical headache disorders. A significant reduction in headache frequency and intensity during a 3 months follow-up was documented. Larger, prospective, randomized, sham-controlled studies are urgently needed to confirm if rNMS may become a new valuable non-invasive, non-pharmacological treatment option for pediatric headache disorders.

Repetitive Neuromuscular Magnetic Stimulation for Pediatric Headache Disorders: Muscular Effects and Factors Affecting Level of Response.

Repetitive neuromuscular magnetic stimulation (rNMS) for pediatric headache disorders is feasible, safe, and alleviates headache symptoms. This study assesses muscular effects and factors affecting response to rNMS. A retrospective chart review included children with headaches receiving six rNMS sessions targeting the upper trapezius muscles. Pressure pain thresholds (PPT) were measured before and after rNMS, and at 3-month follow-up (FU). Mean headache frequency, duration, and intensity within the last 3 months were documented. In 20 patients (14.1 ± 2.7 years), PPT significantly increased from pre- to post-treatment (p < 0.001) sustaining until FU. PPT changes significantly differed between primary headache and post-traumatic headache (PTH) (p = 0.019−0.026). Change in headache frequency was significantly higher in patients with than without neck pain (p = 0.032). A total of 60% of patients with neck pain responded to rNMS (≥25%), while 20% of patients without neck pain responded (p = 0.048). 60% of patients receiving rNMS twice a week were responders, while 33% of patients receiving rNMS less or more frequently responded to treatment, respectively. Alleviation of muscular hyperalgesia was demonstrated sustaining for 3 months, which was emphasized in PTH. The rNMS sessions may positively modulate headache symptoms regardless of headache diagnosis. Patients with neck pain profit explicitly well. Two rNMS sessions per week led to the highest reduction in headache frequency.

Response Predictors of Repetitive Neuromuscular Magnetic Stimulation in the Preventive Treatment of Episodic Migraine.

Background: Repetitive neuromuscular magnetic stimulation (rNMS) of the trapezius muscles showed beneficial effects in preventing episodic migraine. However, clinical characteristics that predict a favorable response to rNMS are unknown. The objective of this analysis is to identify such predictors. Methods: Thirty participants with a diagnosis of episodic migraine (mean age: 24.8 ± 4.0 years, 29 females), who were prospectively enrolled in two non-sham-controlled studies evaluating the effects of rNMS were analyzed. In these studies, the interventional stimulation of the bilateral trapezius muscles was applied in six sessions and distributed over two consecutive weeks. Baseline and follow-up assessments included the continuous documentation of a headache calendar over 30 days before and after the stimulation period, the Migraine Disability Assessment Score (MIDAS) questionnaire (before stimulation and 90 days after stimulation), and measurements of pain pressure thresholds (PPTs) above the trapezius muscles by algometry (before and after each stimulation session). Participants were classified as responders based on a ≥25% reduction in the variable of interest (headache frequency, headache intensity, days with analgesic intake, MIDAS score, left-sided PPTs, right-sided PPTs). Post-hoc univariate and multivariate binary logistic regression analyses were performed. Results: Lower headache frequency (P = 0.016) and intensity at baseline (P = 0.015) and a migraine diagnosis without a concurrent tension-type headache component (P = 0.011) were significantly related to a ≥25% reduction in headache frequency. Higher headache frequency (P = 0.052) and intensity at baseline (P = 0.014) were significantly associated with a ≥25% reduction in monthly days with analgesic intake. Lower right-sided PPTs at baseline were significantly related to a ≥25% increase in right-sided PPTs (P = 0.015) and left-sided PPTs (P =0.030). Performance of rNMS with higher stimulation intensities was significantly associated with a ≥25% reduction in headache intensity (P = 0.046). Conclusions: Clinical headache characteristics at baseline, the level of muscular hyperalgesia, and stimulation intensity may inform about how well an individual patient responds to rNMS. These factors may allow an early identification of patients that would most likely benefit from rNMS.

Genome-wide DNA methylation analysis of archival formalin-fixed paraffin-embedded tissue using the Illumina Infinium HumanMethylation27 BeadChip.

Aberrant DNA methylation of promoter and other genomic regions can lead to changes in gene expression, such as over-expression of oncogenes and the silencing of tumour suppressor genes in the context of cancer. Ability to accurately assess the DNA methylation status is therefore of great importance in health and disease. Recently, various platforms for genome-wide analysis of promoter DNA methylation have been developed, including the Illumina Infinium platform. While some of these platforms can be used with formalin-fixed paraffin-embedded (FFPE) tissue, no protocol has yet been developed for the analysis of FFPE-derived DNA on the Infinium platform using the HumanMethylation27 BeadChip which interrogates 27,578 cytosine-guanine (CpG) dinucleotide sites, selected predominantly from the promoter regions of 14,000 annotated genes. As FFPE preservation has been the method of choice for the archiving of clinical samples, the ability to analyse such samples opens the possibility to study large numbers of clinically well annotated samples which can be expected to lead to more powerful and robust data, particularly for rare cancers. Here, we describe a protocol for the analysis of FFPE samples using the Infinium HumanMethylation27 BeadChip.

The bottom-up approach: Non-invasive peripheral neurostimulation methods to treat migraine: A scoping review from the child neurologist's perspective.

Migraine is a common and invalidating disorder worldwide. Patients of all ages experience the disorder as very impairing regarding their personal and occupational lives. The current approach in migraine therapy is multimodal including lifestyle management, psychoeducation and, if available, psychotherapeutic interventions, and pharmacotherapy. The lack of non-pharmacological and non-invasive treatment options call for new and innovative therapeutic approaches. Peripheral neurostimulation is a relatively new method in migraine management offering a painless and non-pharmacological way of targeting specific mechanisms involved in migraine. This review summarizes 15 recent randomized clinical trials to provide an overview of non-invasive peripheral neurostimulation methods currently available for the treatment of migraine. Efficacy, tolerability, and safety of the different interventions and their feasibility in the pediatric setting are evaluated. Vagal nerve stimulation (VNS), remote electrical neuromodulation (REN) and supraorbital nerve stimulation (SNS) are considered effective in treating acute migraine attacks, the latter being more pronounced in migraine without aura. Regarding migraine prevention, occipital nerve stimulation (ONS) and supraorbital nerve stimulation (SNS) demonstrated efficacy, whereas repetitive neuromuscular magnetic stimulation (rNMS) may represent a further effective option in episodic migraine. REN and rNMS were found to be well-accepted with fewer patients discontinuing treatment than those receiving direct cranial nerve stimulation. In summary, peripheral neurostimulation represents a promising option to complement the multimodal therapy concept for pediatric migraine. In particular, rNMS opens a new field for research and treatment fitting the requirements of "non-invasiveness" for children. Given the reported efficacy, safety, and feasibility, the therapy decision should be made on an individual level.

HOXA11 DNA methylation--a novel prognostic biomarker in ovarian cancer.

Epigenetic alterations play a major role in cancer. Recently we reported that stem cell Polycomb group targets (PcGTs) are up to 12-fold more likely to have cancer-specific promoter DNA hypermethylation than nontargets. To identify potential, prognostic DNA methylation markers in ovarian cancer we analyzed the DNA methylation at 71 different loci in 22 ovarian cancers and 18 non-neoplastic ovarian specimens by means of a quantitative, real-time PCR-based technique (MethyLight). We identified DNA methylation of HOXA10 and HOXA11, both of them PcGTs, to be the best discriminators between cancer and non-neoplastic tissue. In an independent set consisting of 92 ovarian cancer specimens further analysis demonstrated that HOXA11 DNA methylation is (i) strongly associated with the residual tumor after cytoreductive surgery and (ii) is a marker indicating poor prognosis. HOXA11 DNA methylation was independently associated with poor outcome [relative risk for death 3.4 (95% CI 1.2-9.9; p = 0.03)]. These findings support the view that the technical inability to optimally cytoreduce ovarian cancer is associated with particular molecular alterations in the tumor which per se define a subgroup of patients with poor outcome.

CsrA and its regulators control the time-point of ColicinE2 release in Escherichia coli.

The bacterial SOS response is a cellular reaction to DNA damage, that, among other actions, triggers the expression of colicin - toxic bacteriocins in Escherichia coli that are released to kill close relatives competing for resources. However, it is largely unknown, how the complex network regulating toxin expression controls the time-point of toxin release to prevent premature release of inefficient protein concentrations. Here, we study how different regulatory mechanisms affect production and release of the bacteriocin ColicinE2 in Escherichia coli. Combining experimental and theoretical approaches, we demonstrate that the global carbon storage regulator CsrA controls the duration of the delay between toxin production and release and emphasize the importance of CsrA sequestering elements for the timing of ColicinE2 release. In particular, we show that ssDNA originating from rolling-circle replication of the toxin-producing plasmid represents a yet unknown additional CsrA sequestering element, which is essential in the ColicinE2-producing strain to enable toxin release by reducing the amount of free CsrA molecules in the bacterial cell. Taken together, our findings show that CsrA times ColicinE2 release and reveal a dual function for CsrA as an ssDNA and mRNA-binding protein, introducing ssDNA as an important post-transcriptional gene regulatory element.

Interactions mediated by a public good transiently increase cooperativity in growing Pseudomonas putida metapopulations.

Bacterial communities have rich social lives. A well-established interaction involves the exchange of a public good in Pseudomonas populations, where the iron-scavenging compound pyoverdine, synthesized by some cells, is shared with the rest. Pyoverdine thus mediates interactions between producers and non-producers and can constitute a public good. This interaction is often used to test game theoretical predictions on the "social dilemma" of producers. Such an approach, however, underestimates the impact of specific properties of the public good, for example consequences of its accumulation in the environment. Here, we experimentally quantify costs and benefits of pyoverdine production in a specific environment, and build a model of population dynamics that explicitly accounts for the changing significance of accumulating pyoverdine as chemical mediator of social interactions. The model predicts that, in an ensemble of growing populations (metapopulation) with different initial producer fractions (and consequently pyoverdine contents), the global producer fraction initially increases. Because the benefit of pyoverdine declines at saturating concentrations, the increase need only be transient. Confirmed by experiments on metapopulations, our results show how a changing benefit of a public good can shape social interactions in a bacterial population.

Mass spectrometric profiling of low-molecular-weight volatile compounds--diagnostic potential and latest applications.

The theoretical use of mass spectrometric profiling of low-molecular-weight volatile compounds, as one possible method to non-invasively and rapidly diagnose a variety of diseases, such as cancer, infection, and metabolic disorders has greatly raised the profile of this technique over the last ten years. Despite a number of promising results, this technique has not been introduced into common clinical practice yet. The use of mass spectrometric profiling of exhaled air is particularly hampered by various technical problems and basic methodological issues which have only been partially overcome. However, breath analysis aside, recently published studies reveal completely new ideas and concepts on how to establish fast and reliable diagnosis by using this valuable tool. These studies focussed on the headspace screening of various bodily fluids and sample fluids obtained during diagnostic procedures, as well as microbial cell cultures and demonstrated the vast diagnostic potential of this technique in a wide variety of settings, predominantly in vitro. It is the aim of the present review to discuss the most commonly detected low-molecular-weight volatile compounds and to summarize the current potential applications, latest developments and future perspectives of this promising diagnostic approach.

Ecological feedback in quorum-sensing microbial populations can induce heterogeneous production of autoinducers.

Autoinducers are small signaling molecules that mediate intercellular communication in microbial populations and trigger coordinated gene expression via 'quorum sensing'. Elucidating the mechanisms that control autoinducer production is, thus, pertinent to understanding collective microbial behavior, such as virulence and bioluminescence. Recent experiments have shown a heterogeneous promoter activity of autoinducer synthase genes, suggesting that some of the isogenic cells in a population might produce autoinducers, whereas others might not. However, the mechanism underlying this phenotypic heterogeneity in quorum-sensing microbial populations has remained elusive. In our theoretical model, cells synthesize and secrete autoinducers into the environment, up-regulate their production in this self-shaped environment, and non-producers replicate faster than producers. We show that the coupling between ecological and population dynamics through quorum sensing can induce phenotypic heterogeneity in microbial populations, suggesting an alternative mechanism to stochastic gene expression in bistable gene regulatory circuits.

Gender and age specific differences in exhaled isoprene levels.

The analysis of volatile organic compounds (VOC) in the human breath has attracted a considerable amount of clinical and scientific interest during the last decade. In our study, we turned our attention to gender and age specific differences of exhaled volatile compounds, particularly on isoprene which is one of the most abundant organic molecules found in human exhaled air. A total of 126 test persons were enrolled in the study: 66 females and 60 males. Moreover, the participants were classified into six groups with regard to their age. In a standardized setting all of them had to exhale the endexpiratory breath into a sample bag. The volatile compounds at m/z values from 21 to 229 were analyzed by using proton-transfer-reaction-mass-spectrometry. Isoprene (at m/z 69) was found to be highly significantly (p<0.001) elevated in the exhaled air of male subjects. Furthermore, it could be shown that 19-29 years old subjects exhale significantly lower levels of isoprene than older adults (p=0.002). No significant differences between groups were detected for any other measured mass. In conclusion, the present study demonstrates gender and age specific differences of isoprene levels in the exhaled air. These findings may be of potential clinical relevance regarding the multifaceted roles of isoprene, representing both indicator and effector molecule.

Mass spectrometric profile of exhaled breath--field study by PTR-MS.

Recently, increased interest has focused on the diagnostic potential of volatile organic compounds (VOC) exhaled in human breath as this substance group has been conjectured in indoor air quality and disease screening. Proton transfer reaction-mass spectrometry (PTR-MS) has been established as a new tool for a rapid determination of exhaled air profile. However, no investigations have been carried out into the profile of exhaled air as determined by PTR-MS. Therefore, it was the aim of the present study to determine the profile of exhaled breath in a field survey enrolling 344 persons. Analysis was performed using PTR-MS. No significant correlations with age, blood pressure, and body mass index could be observed with any molecular mass. The present study delineates possible reference values for PTR-MS investigations into exhaled air profile. In conclusion, the present study was the first to delineate mass spectrometric characteristics of an average patient sample as possible reference values.

Non-Selective Evolution of Growing Populations.

Non-selective effects, like genetic drift, are an important factor in modern conceptions of evolution, and have been extensively studied for constant population sizes (Kimura, 1955; Otto and Whitlock, 1997). Here, we consider non-selective evolution in the case of growing populations that are of small size and have varying trait compositions (e.g. after a population bottleneck). We find that, in these conditions, populations never fixate to a trait, but tend to a random limit composition, and that the distribution of compositions "freezes" to a steady state. This final state is crucially influenced by the initial conditions. We obtain these findings from a combined theoretical and experimental approach, using multiple mixed subpopulations of two Pseudomonas putida strains in non-selective growth conditions (Matthijs et al, 2009) as model system. The experimental results for the population dynamics match the theoretical predictions based on the Pólya urn model (Eggenberger and Pólya, 1923) for all analyzed parameter regimes. In summary, we show that exponential growth stops genetic drift. This result contrasts with previous theoretical analyses of non-selective evolution (e.g. genetic drift), which investigated how traits spread and eventually take over populations (fixate) (Kimura, 1955; Otto and Whitlock, 1997). Moreover, our work highlights how deeply growth influences non-selective evolution, and how it plays a key role in maintaining genetic variability. Consequently, it is of particular importance in life-cycles models (Melbinger et al, 2010; Cremer et al, 2011; Cremer et al, 2012) of periodically shrinking and expanding populations.

Epigenetics markers of metastasis and HPV-induced tumorigenesis in penile cancer.

PURPOSE: Penile cancer is a rare malignancy in the developed world with just more than 1,600 new cases diagnosed in the United States per year; however, the incidence is much higher in developing countries. Although HPV is known to contribute to tumorigenesis, little is known about the genetic or epigenetic alterations defining penile cancer. EXPERIMENTAL DESIGN: Using high-density genome-wide methylation arrays, we have identified epigenetic alterations associated with penile cancer. Q-MSP was used to validate lymph node metastasis markers in 50 cases. A total of 446 head and neck squamous cell carcinoma (HNSCC) and cervical squamous cell carcinoma (CESCC) samples were used to validate HPV-associated epigenetic alterations. RESULTS: We defined 6,933 methylation variable positions (MVP) between normal and tumor tissue, which includes 997 hypermethylated differentially methylated regions associated with tumor supressor genes, including CDO1, AR1, and WT1. Analysis of penile cancer tumors identified a 4 gene epi-signature which accurately predicted lymph node metastasis in an independent cohort (AUC of 89%). Finally, we explored the epigenetic alterations associated with penile cancer HPV infection and defined a 30 loci lineage-independent HPV specific epi-signature which predicts HPV status and survival in independent HNSCC, CESC cohorts. Epi-signature-negative patients have a significantly worse overall survival [HNSCC P = 0.00073; 95% confidence interval (CI), 0.021-0.78; CESC P = 0.0094; HR = 3.91, 95% CI = 0.13-0.78], HPV epi-signature is a better predictor of survival than HPV status alone. CONCLUSIONS: These data demonstrate for the first time genome-wide epigenetic events involved in an aggressive penile cancer phenotype and define the epigenetic alterations common across multiple HPV-driven malignancies.

Using high-density DNA methylation arrays to profile copy number alterations.

The integration of genomic and epigenomic data is an increasingly popular approach for studying the complex mechanisms driving cancer development. We have developed a method for evaluating both methylation and copy number from high-density DNA methylation arrays. Comparing copy number data from Infinium HumanMethylation450 BeadChips and SNP arrays, we demonstrate that Infinium arrays detect copy number alterations with the sensitivity of SNP platforms. These results show that high-density methylation arrays provide a robust and economic platform for detecting copy number and methylation changes in a single experiment. Our method is available in the ChAMP Bioconductor package: http://www.bioconductor.org/packages/2.13/bioc/html/ChAMP.html.